Bam file without any sequence

Question

[tiago211287]

I have a sam file generated from the conversion of a psl file using psl2sam.pl script. However it has a * placeholder in the place of a sequence. I have tried but fail in find any tool that could retrieve from the fasta, the sequence. Does anyone know any tool/script for doing that?

[mks002]

U can get some help from the blogs at the link here.

Also, u can try first converting your file to bed and then to desired out link sam file. Use the bedops_linux_x86_64-v2.4.25